June 2, 2022
After identifying a total of 48 candidates, I ranked them and selected the top 12 to test in the lab. I did this by assembling gene blocks coding for the antiCRISPR candidate I wanted to test into a pHERD30t plasmid. I then transformed the modified plasmid into Pseudomonas PAO1, a strain of Pseudomonas that has Cas12a activity. Finally, I performed a plaque assay to check if the six candidates I tested exhibited antiCRISPR activity. While unfortunately they did not, I have six more candidates that I'm planning to test over the summer.
October 25, 2021
I had another successful call with Dr. Marino this week. I reviewed the articles she sent and went over some tutorials on how to use NCBI's BLAST computational genome comparison tool. Dr. Marino explained the methods she used in her study in more depth, mainly how she used the guilt-by-association and self-targeting spacers method to identify Acr candidates. We also reviewed the wet-lab methods she used to determine if the candidates were actually Acrs, and if so, whether they function in human cells as well as bacteria.
October 13, 2021
I had a very successful call with Dr. Marino today. She is a postdoc researcher at the Bondy-Denomy lab, studying antiCRISPRs and bacterial immune systems. We discussed the possibility of working with her and potentially coming into her lab to work during breaks and the summer. She also sent me a paper she authored to review before our next meeting, see Relevant Articles.
September 16, 2021
This week I had an encouraging call with Dr. Joseph Bondy Denomy from the Bondy Denomy lab at UCSF. The lab studies the coevolution of bacterial and bacteriophage immune systems, and studies different bacteriophage defense systems that defend phages from CRISPR when infecting a bacterial host. My call went well, and I talked with Dr. Bondy Denomy about the potential to work in his lab intermittently throughout the school year and as a full time job over the summer. I also have a call scheduled with Dr. Kevin Yehl, an author of one of the important papers that have impacted my project.
August 30, 2021
School started last week, and I have been enjoying getting back into the lab in my Advanced Chemistry, Anatomy and Physiology, and Advanced Physics classes. I have also started to get back into the independent research headspace by reviewing my work from last year and reading recent articles related to phage engineering - mainly looking for protocols to use for data collection. My goals for this month are to: write a general experimental plan and list materials, fit a timeline to the plan, find/create protocols to use in the lab, and begin familiarizing myself with Benchling for plasmid construction.
July 24, 2021
After coming home from Boston, I began my summer course in molecular engineering. The course mainly focuses on engineering the dye particles of dye-sensitized solar cells (DSSCs) to be more efficient at capturing visible light and transforming it into electrical energy. To do this, I have constructed various DSSCs using different sources of anthocyanins. Additionally, I learned how to access UChicago's HBCC supercomputer to run simulations of different alterations to anthocyanin dye and analyze the effect that the molecular modification had on DSCC efficacy.
June 22, 2021
This week I started my Neuroscience and Neurosurgery program at the Boston Leadership Institute. We have mainly discussed an overview of neurons and glial cells, common neurotransmitters, and how different parts of the nervous system are affected by disorders like Alzheimer's, Multiple Sclerosis, and Huntington's Disease. Some lab work that we have performed was to simulate the blood-brain barrier.
June 1, 2021
I'm wrapping up junior year, with only one day left of school to go. Over the summer, I'll be completing the Boston Leadership Institute's Neuroscience and Neurosurgery Research program, and UChicago's Pathways in Molecular engineering course. I also plan to familiarize myself with the Benchling software for creating custom plasmids, begin to explore Python, and continue work from this year like my project proposal and mentor outreach.
May 24, 2021
Last MARC class of the year š. Today the IR1 cohort shared posters and videos describing all of our work this year with the senior MARCers and some staff members. It was great to see how everyone's project's had evolved over the year, and I enjoyed synthesizing all of my work into a single poster.
May 16, 2021
This week I followed up with Doctors Joel Ernst and Paul Ogongo from UCSF, who Dr. Kumar had introduced me to via email. While they are unable to have high school interns in their lab, they provided me with some contacts at UCSF's Bondy-Denomy lab who I have reached out to.
May 14, 2021
This week I spent a lot of time reading literature and descriptions of the work of researchers at ZSFG and Vitalent, two research centers dealing with immunology. I also talked with Dr. Nitasha Kumar to discuss strategies for mentor outreach, and she informed me of the Bondy-Denomy Lab at UCSF. The lab deals with phages, specifically studying how defense mechanisms encoded by bacteria target phages and how phages co-evolve to deal with that pressure. I plan to contact researchers from the lab about a potential mentorship.
May 6, 2021
So far this week, I have finalized the Background section of my project proposal, written an Abstract, and have started to work on the specific aims and hypotheses. I also decided to compare BRED with CRISPR-Cas-mediated engineering, as using a Yeast-Based platform would be more time consuming, less feasible, and less likely to produce significant results in the time period available.
April 28, 2021
I'm currently working on completing the Research Description of my project proposal, and am spending a lot of time looking through journal articles for standard BRED and CRISPR-Cas-based standard engineering protocols. I have found a protocol for Yeast-Based engineering, and am trying to decide whether or not it would e feasible to use this system in the MA lab.